| Nucleotide polymorphism |
|
| Number of segregating sites (S, s) |
Nei (9) |
| Minimum number of mutations (H, η) |
Tajima (10) |
| Nucleotide diversity (π) (with and without Jukes and Cantor correction) |
Nei (9); Jukes and Cantor (11) |
| Theta (θ) per DNA sequence from S |
Tajima (12) |
| Theta (θ) per site from S |
Nei (9) |
| Theta (θ) per site from Eta (η) |
Tajima (10) |
| Theta (θ) per site from π, from S and from η under the Finite Sites Model |
Tajima (10) |
| Average number of nucleotide differences (k) |
Tajima (13) |
| Tajima statistic test (D) |
Tajima (14) |
| Total number of synonymous and non-synonymous sites |
Nei and Gojobori (15) |
| Number of non-synonymous substitutions per non-synonymous site (Ka) and number of synonymous substitutions per synonymous site (Ks) |
Nei and Gojobori (15) |
| Codon bias |
|
| Relative Synonymous Codon Usage (RSCU) |
Sharp (16) |
| Effective Number of Codons (ENC) |
Wright (17) |
| Codon Adaptation Index (CAI) |
Sharp and Li (18) |
| Scaled Chi Square |
Shields (19) |
| G + C content in second, third and total positions |
Wright (17) |
| Linkage disequilibrium |
|
| Nucleotide distance (Dist) between a pair of polymorphic sites |
|
| D |
Lewontin and Kojima (20) |
| D′ |
Lewontin (21) |
| R and R2
|
Hill and Robertson (22) |
| ZnS statistic |
Kelly (23) |
| Chi-square test |
|
| Fisher's exact test |
|
